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- PDB-6e0t: C-terminal domain of Fission Yeast OFD1 -

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Basic information

Entry
Database: PDB / ID: 6e0t
TitleC-terminal domain of Fission Yeast OFD1
ComponentsProlyl 3,4-dihydroxylase ofd1
KeywordsCYTOSOLIC PROTEIN / prolyl hydrolase sterol synthesis
Function / homology
Function and homology information


negative regulation of transcription by transcription factor catabolism / peptidyl-proline hydroxylation / peptidyl-proline di-hydroxylation / negative regulation of SREBP signaling pathway / cellular response to hyperoxia / peptidyl-proline dioxygenase activity / negative regulation of cellular response to hypoxia / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / L-ascorbic acid binding ...negative regulation of transcription by transcription factor catabolism / peptidyl-proline hydroxylation / peptidyl-proline di-hydroxylation / negative regulation of SREBP signaling pathway / cellular response to hyperoxia / peptidyl-proline dioxygenase activity / negative regulation of cellular response to hypoxia / regulation of translational termination / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / L-ascorbic acid binding / oxygen sensor activity / negative regulation of DNA binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / iron ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
Prolyl 3,4-dihydroxylase ofd1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.02 Å
AuthorsBianchet, M.A. / Amzel, L.M. / Espenshade, P.J. / Yeh, T.
CitationJournal: Structure / Year: 2011
Title: The hypoxic regulator of sterol synthesis nro1 is a nuclear import adaptor.
Authors: Yeh, T.L. / Lee, C.Y. / Amzel, L.M. / Espenshade, P.J. / Bianchet, M.A.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Prolyl 3,4-dihydroxylase ofd1


Theoretical massNumber of molelcules
Total (without water)30,3741
Polymers30,3741
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.085, 106.717, 64.649
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-706-

HOH

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Components

#1: Protein Prolyl 3,4-dihydroxylase ofd1 / 2-oxoglutarate and Fe(II) dioxygenase domain-containing protein 1 / PKHD-type hydroxylase ofd1 / ...2-oxoglutarate and Fe(II) dioxygenase domain-containing protein 1 / PKHD-type hydroxylase ofd1 / uS12 prolyl 3 / 4-dihydroxylase


Mass: 30374.283 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: ofd1, SPBC6B1.08c / Production host: Escherichia coli (E. coli)
References: UniProt: Q11120, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.57 % / Description: 1 x 1 x 30 uM^3
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.2 M LiSo4, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54184 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 12, 2010 / Details: Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.02→29.091 Å / Num. obs: 18232 / % possible obs: 96.9 % / Redundancy: 6.8 % / Rsym value: 0.066 / Net I/σ(I): 28
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 4.9 % / Num. unique obs: 756 / Rsym value: 0.368 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.02→29.091 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2437 934 5.12 %
Rwork0.2002 --
obs0.2024 18229 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.02→29.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 0 156 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032069
X-RAY DIFFRACTIONf_angle_d0.9162819
X-RAY DIFFRACTIONf_dihedral_angle_d14.493768
X-RAY DIFFRACTIONf_chiral_restr0.034308
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0205-2.1270.28241180.22562118X-RAY DIFFRACTION86
2.127-2.26020.32081310.27252508X-RAY DIFFRACTION99
2.2602-2.43460.23971320.24062490X-RAY DIFFRACTION99
2.4346-2.67950.28361500.23562510X-RAY DIFFRACTION100
2.6795-3.06680.32451270.23882473X-RAY DIFFRACTION98
3.0668-3.86240.21691420.18082562X-RAY DIFFRACTION100
3.8624-29.0940.20311340.16342634X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.0972 Å / Origin y: -15.7596 Å / Origin z: -9.1251 Å
111213212223313233
T0.2207 Å2-0.0259 Å20.0211 Å2-0.2542 Å2-0.0227 Å2--0.2376 Å2
L1.4311 °20.3096 °2-0.0468 °2-2.3697 °2-0.2488 °2--1.6139 °2
S-0.0389 Å °-0.0572 Å °-0.1545 Å °-0.0831 Å °-0.0036 Å °0.2149 Å °0.1215 Å °-0.1544 Å °0.0152 Å °
Refinement TLS groupSelection details: all

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